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Magnesium in PDB 2ihv: Carboxyethylarginine Synthase From Streptomyces Clavuligerus: 5- Guanidinovaleric Acid Complex

Enzymatic activity of Carboxyethylarginine Synthase From Streptomyces Clavuligerus: 5- Guanidinovaleric Acid Complex

All present enzymatic activity of Carboxyethylarginine Synthase From Streptomyces Clavuligerus: 5- Guanidinovaleric Acid Complex:
2.5.1.66;

Protein crystallography data

The structure of Carboxyethylarginine Synthase From Streptomyces Clavuligerus: 5- Guanidinovaleric Acid Complex, PDB code: 2ihv was solved by M.E.Caines, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.15 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 120.744, 128.297, 197.638, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 19.2

Other elements in 2ihv:

The structure of Carboxyethylarginine Synthase From Streptomyces Clavuligerus: 5- Guanidinovaleric Acid Complex also contains other interesting chemical elements:

Potassium (K) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Carboxyethylarginine Synthase From Streptomyces Clavuligerus: 5- Guanidinovaleric Acid Complex (pdb code 2ihv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Carboxyethylarginine Synthase From Streptomyces Clavuligerus: 5- Guanidinovaleric Acid Complex, PDB code: 2ihv:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2ihv

Go back to Magnesium Binding Sites List in 2ihv
Magnesium binding site 1 out of 4 in the Carboxyethylarginine Synthase From Streptomyces Clavuligerus: 5- Guanidinovaleric Acid Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Carboxyethylarginine Synthase From Streptomyces Clavuligerus: 5- Guanidinovaleric Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:5.9
occ:1.00
OD1 A:ASN490 2.1 25.8 1.0
O1A A:TPP600 2.2 18.8 1.0
OD1 A:ASP463 2.3 19.1 1.0
O A:THR492 2.3 22.7 1.0
O A:HOH662 2.3 19.3 1.0
O3B A:TPP600 2.4 17.4 1.0
CG A:ASP463 3.3 19.5 1.0
CG A:ASN490 3.3 26.0 1.0
PA A:TPP600 3.4 17.6 1.0
C A:THR492 3.5 23.2 1.0
PB A:TPP600 3.5 19.1 1.0
O3A A:TPP600 3.7 18.6 1.0
OD2 A:ASP463 3.7 19.8 1.0
O7 A:TPP600 4.0 19.0 1.0
N A:GLY494 4.0 21.8 1.0
N A:THR492 4.1 24.1 1.0
N A:ASP463 4.1 19.0 1.0
ND2 A:ASN490 4.1 26.9 1.0
N A:ASN490 4.2 24.1 1.0
O1B A:TPP600 4.3 21.3 1.0
CA A:THR492 4.3 23.7 1.0
N A:GLY464 4.4 19.7 1.0
CB A:ASN490 4.4 24.7 1.0
N A:ASN493 4.5 22.9 1.0
CB A:ASP463 4.5 19.4 1.0
O A:VAL488 4.5 22.1 1.0
CA A:ASN490 4.6 24.8 1.0
O2A A:TPP600 4.6 17.4 1.0
CA A:ASN493 4.6 22.4 1.0
CB A:THR492 4.7 23.7 1.0
CA A:GLY494 4.7 21.3 1.0
O2B A:TPP600 4.7 19.2 1.0
C A:ASN490 4.8 24.8 1.0
CA A:ASP463 4.8 19.5 1.0
N A:ASP491 4.8 25.4 1.0
C A:ASN493 4.9 22.0 1.0
CA A:GLY462 4.9 18.5 1.0
C A:GLY462 4.9 18.8 1.0
OH A:TYR561 4.9 33.2 1.0
CE2 A:TYR561 5.0 33.5 1.0

Magnesium binding site 2 out of 4 in 2ihv

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Magnesium binding site 2 out of 4 in the Carboxyethylarginine Synthase From Streptomyces Clavuligerus: 5- Guanidinovaleric Acid Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Carboxyethylarginine Synthase From Streptomyces Clavuligerus: 5- Guanidinovaleric Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:6.7
occ:1.00
O3B B:TPP600 2.2 24.5 1.0
OD1 B:ASN490 2.2 26.8 1.0
O1A B:TPP600 2.3 21.6 1.0
OD1 B:ASP463 2.3 22.0 1.0
O B:THR492 2.3 23.4 1.0
O B:HOH1068 2.4 20.3 1.0
CG B:ASP463 3.4 21.0 1.0
CG B:ASN490 3.4 26.0 1.0
PA B:TPP600 3.4 21.2 1.0
PB B:TPP600 3.5 22.8 1.0
C B:THR492 3.5 23.6 1.0
O3A B:TPP600 3.7 24.2 1.0
OD2 B:ASP463 3.8 21.4 1.0
O7 B:TPP600 4.0 23.0 1.0
N B:ASP463 4.1 20.1 1.0
N B:GLY494 4.1 21.8 1.0
N B:THR492 4.1 24.5 1.0
N B:ASN490 4.1 24.4 1.0
O1B B:TPP600 4.2 24.9 1.0
ND2 B:ASN490 4.2 26.4 1.0
CA B:THR492 4.3 23.9 1.0
N B:GLY464 4.4 19.5 1.0
O B:VAL488 4.4 22.4 1.0
CB B:ASN490 4.4 25.0 1.0
N B:ASN493 4.6 23.3 1.0
CB B:ASP463 4.6 19.9 1.0
O2B B:TPP600 4.6 21.1 1.0
CA B:ASN490 4.6 24.8 1.0
CB B:THR492 4.6 24.1 1.0
OH B:TYR561 4.7 34.4 1.0
O2A B:TPP600 4.7 23.8 1.0
C B:ASN490 4.7 24.9 1.0
CA B:ASP463 4.7 19.9 1.0
N B:ASP491 4.7 25.3 1.0
CA B:GLY494 4.7 21.2 1.0
CA B:ASN493 4.8 22.6 1.0
CE2 B:TYR561 4.8 34.7 1.0
C B:GLY462 4.8 20.0 1.0
CA B:GLY462 4.8 19.4 1.0
C B:ASN493 5.0 22.1 1.0

Magnesium binding site 3 out of 4 in 2ihv

Go back to Magnesium Binding Sites List in 2ihv
Magnesium binding site 3 out of 4 in the Carboxyethylarginine Synthase From Streptomyces Clavuligerus: 5- Guanidinovaleric Acid Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Carboxyethylarginine Synthase From Streptomyces Clavuligerus: 5- Guanidinovaleric Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:10.4
occ:1.00
OD1 C:ASN490 2.2 26.2 1.0
O1A C:TPP600 2.2 23.3 1.0
O3B C:TPP600 2.3 24.0 1.0
O C:HOH1108 2.3 21.2 1.0
OD1 C:ASP463 2.3 23.3 1.0
O C:THR492 2.4 24.7 1.0
CG C:ASP463 3.4 20.3 1.0
CG C:ASN490 3.4 26.0 1.0
PA C:TPP600 3.4 23.8 1.0
PB C:TPP600 3.5 23.8 1.0
C C:THR492 3.5 24.8 1.0
O3A C:TPP600 3.7 24.8 1.0
OD2 C:ASP463 3.8 21.0 1.0
O7 C:TPP600 4.0 25.6 1.0
N C:THR492 4.1 25.7 1.0
N C:ASN490 4.1 24.2 1.0
N C:ASP463 4.1 19.5 1.0
N C:GLY494 4.1 23.2 1.0
ND2 C:ASN490 4.2 28.1 1.0
O1B C:TPP600 4.2 23.2 1.0
CA C:THR492 4.3 25.3 1.0
CB C:ASN490 4.4 24.9 1.0
O C:VAL488 4.4 22.1 1.0
N C:GLY464 4.4 19.6 1.0
CA C:ASN490 4.6 24.7 1.0
N C:ASN493 4.6 24.4 1.0
CB C:ASP463 4.6 19.9 1.0
CB C:THR492 4.7 25.7 1.0
O2B C:TPP600 4.7 23.0 1.0
OH C:TYR561 4.7 34.3 1.0
O2A C:TPP600 4.7 23.9 1.0
C C:ASN490 4.7 25.1 1.0
CE2 C:TYR561 4.7 34.5 1.0
CA C:ASN493 4.8 23.8 1.0
N C:ASP491 4.8 25.8 1.0
CA C:ASP463 4.8 19.6 1.0
CA C:GLY494 4.8 22.5 1.0
CA C:GLY462 4.8 19.0 1.0
C C:GLY462 4.9 19.3 1.0
C C:ASN493 5.0 23.1 1.0

Magnesium binding site 4 out of 4 in 2ihv

Go back to Magnesium Binding Sites List in 2ihv
Magnesium binding site 4 out of 4 in the Carboxyethylarginine Synthase From Streptomyces Clavuligerus: 5- Guanidinovaleric Acid Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Carboxyethylarginine Synthase From Streptomyces Clavuligerus: 5- Guanidinovaleric Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:8.0
occ:1.00
OD1 D:ASN490 2.1 25.4 1.0
O D:HOH739 2.2 20.9 1.0
O3B D:TPP600 2.2 21.1 1.0
OD1 D:ASP463 2.2 20.8 1.0
O D:THR492 2.3 24.1 1.0
O1A D:TPP600 2.3 21.0 1.0
CG D:ASN490 3.3 26.2 1.0
CG D:ASP463 3.4 19.9 1.0
PA D:TPP600 3.4 19.8 1.0
PB D:TPP600 3.5 20.8 1.0
C D:THR492 3.5 24.2 1.0
O3A D:TPP600 3.7 22.7 1.0
OD2 D:ASP463 3.9 18.8 1.0
N D:ASP463 4.1 19.5 1.0
N D:GLY494 4.1 22.6 1.0
N D:ASN490 4.1 24.1 1.0
N D:THR492 4.1 24.9 1.0
O7 D:TPP600 4.1 24.0 1.0
O1B D:TPP600 4.1 23.2 1.0
ND2 D:ASN490 4.2 27.4 1.0
CA D:THR492 4.3 24.5 1.0
CB D:ASN490 4.3 24.6 1.0
N D:GLY464 4.4 19.3 1.0
O D:VAL488 4.4 21.5 1.0
N D:ASN493 4.5 23.9 1.0
CB D:ASP463 4.5 19.1 1.0
CA D:ASN490 4.5 24.7 1.0
O2A D:TPP600 4.6 23.9 1.0
O2B D:TPP600 4.7 23.2 1.0
CB D:THR492 4.7 24.2 1.0
CA D:ASN493 4.7 23.4 1.0
CA D:ASP463 4.7 19.5 1.0
C D:ASN490 4.8 25.0 1.0
CA D:GLY494 4.8 22.2 1.0
N D:ASP491 4.8 25.4 1.0
C D:GLY462 4.8 19.4 1.0
CA D:GLY462 4.8 19.2 1.0
C D:ASN493 4.9 22.9 1.0
OH D:TYR561 5.0 33.6 1.0

Reference:

M.E.Caines, J.L.Sorensen, C.J.Schofield. Structural and Mechanistic Studies on N(2)-(2-Carboxyethyl)Arginine Synthase. Biochem.Biophys.Res.Commun. V. 385 512 2009.
ISSN: ISSN 0006-291X
PubMed: 19477162
DOI: 10.1016/J.BBRC.2009.05.095
Page generated: Mon Dec 14 07:27:22 2020

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